8-67509763-T-C
Position:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020361.5(CPA6):c.433-145A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 465,930 control chromosomes in the GnomAD database, including 39,952 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.46 ( 17656 hom., cov: 32)
Exomes 𝑓: 0.36 ( 22296 hom. )
Consequence
CPA6
NM_020361.5 intron
NM_020361.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.551
Genes affected
CPA6 (HGNC:17245): (carboxypeptidase A6) The gene encodes a member of the peptidase M14 family of metallocarboxypeptidases. The encoded preproprotein is proteolytically processed to generate the mature enzyme, which catalyzes the release of large hydrophobic C-terminal amino acids. This enzyme has functions ranging from digestion of food to selective biosynthesis of neuroendocrine peptides. Mutations in this gene may be linked to epilepsy and febrile seizures, and a translocation t(6;8)(q26;q13) involving this gene has been associated with Duane retraction syndrome. [provided by RefSeq, May 2016]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPA6 | NM_020361.5 | c.433-145A>G | intron_variant | ENST00000297770.10 | |||
CPA6 | XM_017013646.2 | c.-12-145A>G | intron_variant | ||||
CPA6 | XM_017013647.2 | c.433-145A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPA6 | ENST00000297770.10 | c.433-145A>G | intron_variant | 1 | NM_020361.5 | P1 | |||
CPA6 | ENST00000479862.6 | c.*29-145A>G | intron_variant, NMD_transcript_variant | 1 | |||||
CPA6 | ENST00000518549.1 | n.647-145A>G | intron_variant, non_coding_transcript_variant | 1 | |||||
CPA6 | ENST00000638254.1 | c.*29-145A>G | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.459 AC: 69757AN: 151922Hom.: 17619 Cov.: 32
GnomAD3 genomes
AF:
AC:
69757
AN:
151922
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.364 AC: 114396AN: 313890Hom.: 22296 AF XY: 0.363 AC XY: 58980AN XY: 162320
GnomAD4 exome
AF:
AC:
114396
AN:
313890
Hom.:
AF XY:
AC XY:
58980
AN XY:
162320
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.459 AC: 69835AN: 152040Hom.: 17656 Cov.: 32 AF XY: 0.455 AC XY: 33804AN XY: 74310
GnomAD4 genome
AF:
AC:
69835
AN:
152040
Hom.:
Cov.:
32
AF XY:
AC XY:
33804
AN XY:
74310
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1153
AN:
3462
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at